starbase is a database and toolkit for exploring of large transposable elements in Fungi

• Owner:
  Adrian Forsythe

Dashboard for the R4A Expertise KG

• Owner:
  Yojana Gadiya

This app allows users to input an image (in jpeg format) of a flower and get a prediction on what type of flower it is from a machine learning model. Top three most likely flower types according to the model’s prediction are shown.

• Owner:
  Arnold Kochari

Biome-specific gene catalogues have been recovered for many environments using shotgun metagenomics, followed by assembly and gene calling on the assembled contigs. We recently proposed a novel mix-assembly strategy, combining individual and co-assembly approaches, and used this approach to assemble an extensive non-redundant gene set from 124 Bal...tic Sea metagenome samples. The Baltic Sea Gene Set (BAGS v1.1) comprises 66.53 million functionally and taxonomically annotated genes. To enable interactive exploration of this gene catalogue we have developed an RShiny application, BAGS-Shiny, that allows users to perform searches by sequence similarity (BLAST) and/or taxonomic and functional annotation. The gene catalogue and web application will serve as valuable tools for exploring microbial gene functions in brackish ecosystems. [see more]

• Owner:
  Luis Fernando Delgado Zambrano

All the browsable datasets from Lee et al 2024. "Open source, high throughput, targeted in situ transcriptomics"

• Owner:
  Marco Grillo

Dashboard plotting the number of people in Sweden aged 0-19 who have have filled a prescription for ADHD medication each year.

• Owner:
  Arnold Kochari

This dashboard visualises the spread of COVID-19 in Sweden: confirmed cases, ICU admissions, and deaths between February 2020 and March 2023.

• Owner:
  Arnold Kochari

Conformal regression model for predicting LogD for drug-like molecules, trained on ChEMBL version 33 with over 2.2M compounds using the CPSign software.

• Owner:
  Staffan Arvidsson McShane

Predicts Ames Mutagenicity for a chemical structure using an SVM model with Signatures features via the CPSign modeling tool.

• Owner:
  Ola Spjuth

RepurposeDrugs - an interactive web-based data portal and predictive platform for repurposing mono- and combination therapies.

• Owner:
  Aleksandr Kushnir

Modelling of cell-type signatures in the developmental human heart

• Owner:
  Christophe Avenel

Comparing 4 types of the most common reference populations for child sex- and age-adjusted Body Mass Index (BMI)

• Owner:
  Maja Engsner

Human heart development ISS datasets generated for Lazar et.al 2024.

• Owner:
  Sergio Marco Salas

Colorectal cancer usually metastasizes in the liver. Tumor cells can create two types of metastases: desmoplastic (DHGP) or replacement (RHGP). DHGP is characterized by a fibrotic rim that encapsulates the tumor cells and is associated with a better survival. In this project, we found two distinct areas in the rim: an outer area representing a ben...ign fibrotic reaction, and an inner area modified by the neighboring cancer cells. [see more]

• Owner:
  Axel Andersson

ALLIUM (ALL subtype Identification Using Machine learning) is a multimodal classifier of molecular subtypes in pediatric acute lymphoblastic leukemia, using DNA methylation (DNAm) and gene expression (GEX) data

• Owner:
  Mariya Lysenkova Wiklander

Correlation Network

• Owner:
  Luay Aswad

Single Protein Localization

• Owner:
  Luay Aswad

Network

• Owner:
  Luay Aswad

Data Download

• Owner:
  Luay Aswad

Heatmap

• Owner:
  Luay Aswad

Application that allows users to get predictive data about compound (Multiple Molecules)

• Owner:
  Hamza Saeed

Application that allows users to get predictive data about compound (Single Molecule)

• Owner:
  Hamza Saeed

Demo of ROC curves, PR curves, and decision boundaries for teaching purposes, www.henlab.org. By Johan Henriksson. Source at https://github.com/henriksson-lab/demo_roc

• Owner:
  Johan Henriksson

Demo of xgboost and decision trees for teaching purposes. By Johan Henriksson, www.henlab.org. Source at https://github.com/henriksson-lab/demo_xgboost

• Owner:
  Johan Henriksson

DICTrank Predictor is an open-source app framework built specifically for human drug-induced cardiotoxicity (DICT).DICTrank Predictor employs physicochemical parameters as feature. For more details look at https://www.biorxiv.org/content/10.1101/2023.10.15.562398v1

• Owner:
  Hamza Saeed

DILI Predictor is an open-source app framework built specifically for human drug-induced liver injury (DILI). DILI Predictor employs eleven proxy-DILI labels from in vitro and in vivo datasets along with pharmacokinetic parameters, structural fingerprints and physicochemical parameters as features.

• Owner:
  Hamza Saeed

API for model that predicts water–octanol distribution coefficient (logD) for chemical compounds: It is a proxy for the lipophilicity which is a major determinant of drug properties and overall suitability of drug candidates

• Owner:
  Hamza Saeed

PK Predictor is an open-source app framework built specifically for predicting human and animal PK parameters

• Owner:
  Hamza Saeed

A Shiny webapp for creating a Seurat object without programming expertise. Load a count matrix directory, interactively filter on metadata, view results, download Seurat object and results of differential gene expression testing.

• Owner:
  Rasmus Olofzon

Demo of clustering with Leiden for teaching purposes. By Johan Henriksson, www.henlab.org. Source at https://github.com/henriksson-lab/demo_clustering

• Owner:
  Johan Henriksson

Demo of penalized linear models (elastic net) for teaching purposes. By Johan Henriksson, www.henlab.org. Source at https://github.com/henriksson-lab/demo_elasticnet

• Owner:
  Johan Henriksson

Demo of Bayesian linear models for teaching purposes. By Johan Henriksson, www.henlab.org. Source at https://github.com/henriksson-lab/demo_bayesianlinmod

• Owner:
  Johan Henriksson

Demo of Bayesian updating for teaching purposes. By Johan Henriksson, www.henlab.org. Source at https://github.com/henriksson-lab/demo_bayesupdate

• Owner:
  Johan Henriksson

scRNASeq of 55 samples from zebrafish brain. This project aims to characterize expression profile of different cell types.

• Owner:
  Nima Rafati

Demo of markov chains and HMMs for teaching purposes. By Johan Henriksson, www.henlab.org. Source at https://github.com/henriksson-lab/demo_markovchain

• Owner:
  Johan Henriksson

Demo of the Poisson distribution, as relevant for NGS, for teaching purposes, www.henlab.org. By Johan Henriksson. Source at https://github.com/henriksson-lab/demo_poisson

• Owner:
  Johan Henriksson

Demo of statistical distributions for teaching purposes. By Johan Henriksson, www.henlab.org. Source at https://github.com/henriksson-lab/demo_statdist

• Owner:
  Johan Henriksson

Co-occurrence plots created using VOS viewer . There are three plots in total, each based on publications from a different SciLifeLab reporting group (i.e. affiliated researchers, infrastructure units, and SciLifeLab fellows). In each plot, we have considered the KeyWords Plus associated with each paper.

• Owner:
  Senthilkumar Panneerselvam

Predicting chemical ecotoxiticy using AI. DOI: https://doi.org/10.1101/2023.04.17.537138

• Owner:
  Käll Styrbjörn

An app to check color balance in indexes for sequencing

• Owner:
  Alma Hansen

Shiny app for exploration of the Genome-wide PeptidoGlycan Profiling dataset of Vibrio cholerae mutant library. Access to this app is password protected while it is under peer review.

• Owner:
  Laura Alvarez

The mappings are provided for genes, proteins, metabolites, metabolic reactions, diseases, complexes and publications. This is a REST service for programmatic access to BridgeDb content, provided with interactive Swagger documentation using OpenAPI. For more info see https://www.bridgedb.org/.

• Owner:
  Arnold Kochari

Service that provides a REST Api to convert between different chemical notations. More info: https://github.com/DouglasConnect/ChemIdConvert.

• Owner:
  Hamza Saeed

Supplemental interactive visualization of Adipose Tissue Gene expression after exercise. Built using flexdashboard.

• Owner:
  Leonidas Lundell

API for Predicting Off-Target Binding Profiles With Confidence Using Conformal Prediction. Refer to https://doi.org/10.3389/fphar.2018.01256 for the paper describing the tool.

• Owner:
  Hamza Saeed

A tool to predict the risk of experiencing refractory/relapse disease within two years in DLBCL patients treated with R-CHOP.

• Owner:
  Hui Wan

Power analysis for RNA-Seq experiment. Estimate number of samples required and more.

• Owner:
  Roy Francis

Imminent myocardial infarction prediction model. In patients free from prior cardiovascular disease, we aimed to identify characteristics of an imminent first heart attack and design a prediction model.

• Owner:
  Stefan Gustafsson

This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

• Owner:
  Lu Pan

This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

• Owner:
  Lu Pan

This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

• Owner:
  Lu Pan

This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

• Owner:
  Lu Pan

This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

• Owner:
  Lu Pan

This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

• Owner:
  Lu Pan

This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

• Owner:
  Lu Pan

This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

• Owner:
  Lu Pan

This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

• Owner:
  Lu Pan

This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

• Owner:
  Lu Pan

This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

• Owner:
  Lu Pan

This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

• Owner:
  Lu Pan

This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

• Owner:
  Lu Pan

This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

• Owner:
  Lu Pan

A single shiny solution from sequencer data to pathway analysis

• Owner:
  Jyotirmoy Das

This Shiny app is used the course CB2030 Systems biology at KTH Royal Instute of Technology.

• Owner:
  Thanadol Sutantiwanichkul

IFNB single-cell transcriptomics data

• Owner:
  Roy Francis

Trancriptom analysis for Suprcellfactories project

• Owner:
  Rasool Saghaleyni

CellChat's Shiny app which allows interactive exploration of the cell-cell communication that are analyzed by the CellChat R-package

• Owner:
  Christophe Avenel

CoViMAPP (CoViD-19 Meta-Analysis of Plasma Proteins) is a meta-analysis resource of plasma proteins' alterations in COVID-19.

• Owner:
  Haris Babacic

OmicLoupe server. See https://quantitativeproteomics.org/omicloupe/ for info about OmicLoupe.

• Owner:
  Fredrik Levander

3D igraph from tsne with variable genes (Data from Tiklova et al. 2016)

• Owner:
  Nanjiang Shu

CitizenScience Project

• Owner:
  Nanjiang Shu

Meta-analysis of skeletal muscle response to exercise and inactivity

• Owner:
  Nicolas Pillon

Single cell RNA sequencing dataset associated with the manuscript "Amnion signals are essential for mesoderm formation in primates"

• Owner:
  Nanjiang Shu

scRNA-seq data in: Small molecule screen identifies a salt-inducible kinase inhibitor inducing β-cell proliferation by transiently activating the unfolded protein response

• Owner:
  Nanjiang Shu

Byrnes, Lauren E., et al. Lineage dynamics of murine pancreatic development at single-cell resolution

• Owner:
  Nanjiang Shu

Companion resource to the article, 'An online atlas of human plasma metabolite signatures of gut microbiome composition' by Dekkers et al

• Owner:
  Koen Dekkers

The Boreal Rhizospheric Atlas online tool was created to encourage exploration of a metatranscriptomic dataset of Norway spruce fine roots and their associated fungal communities from nutrient limited and nutrient enriched forest plots of the boreal region of Northern Sweden.

• Owner:
  Nicolas Delhomme

The Mouse Organ Metabolite Atlas

• Owner:
  Tomasz Czuba